SMTL ID : 1ogy.1 (7 other biounits)

Crystal structure of the heterodimeric nitrate reductase from Rhodobacter sphaeroides

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

hetero-1-1-mer

Ligands

1 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.1: 11 residues within 4Å: Chain A: C.19, F.21, C.22, G.25, C.26, N.53, C.54, K.56, G.57, P.194, I.195 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.19, A:C.22, A:C.26, A:C.54

1 x MO: MOLYBDENUM ATOM(Non-covalent)

MO.2: 5 residues within 4Å: Chain A: C.152, G.383, Q.384 Ligands: MGD.3, MGD.4 Ligand excluded by PLIP

2 x MGD: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE(Non-covalent)

MGD.3: 35 residues within 4Å: Chain A: R.20, Q.123, N.148, H.151, C.152, M.346, Q.350, Q.384, V.454, N.455, N.456, N.457, A.460, S.482, D.483, A.484, T.487, A.499, A.500, M.501, K.505, D.532, T.692, R.694, W.699, H.700, S.701, S.703, M.704, W.768, N.776, F.792, K.793 Ligands: MO.2, MGD.4 28 PLIP interactions: 28 interactions with chain A Hydrogen bonds: A:R.20, A:Q.123, A:N.148, A:Q.350, A:V.454, A:N.455, A:N.456, A:N.456, A:A.460, A:S.482, A:A.484, A:T.487, A:W.502, A:R.694, A:R.694, A:S.701, A:S.703, A:S.703, A:N.776, A:N.776, A:K.793 Salt bridges: A:D.483, A:D.532, A:H.700, A:H.700 pi-Stacking: A:W.768, A:F.792 pi-Cation interactions: A:W.768 MGD.4: 35 residues within 4Å: Chain A: K.56, C.152, W.185, G.186, S.187, N.188, E.191, M.192, S.216, T.217, F.218, H.220, F.232, P.234, G.235, D.237, T.345, M.346, G.347, F.348, G.383, Q.384, V.691, T.692, G.693, R.694, V.695, L.696, H.698, W.699, H.700, K.793, K.794 Ligands: MO.2, MGD.3 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:K.56, A:W.185, A:N.188, A:E.191, A:M.192, A:S.216, A:T.217, A:T.217, A:G.235, A:M.346, A:G.347, A:R.694, A:R.694, A:R.694, A:H.698, A:H.700, A:H.700, A:K.794 Salt bridges: A:D.237, A:R.694, A:K.793 pi-Stacking: A:F.232

2 x HEC: HEME C(Covalent)

HEC.5: 16 residues within 4Å: Chain B: R.30, R.33, P.40, V.41, I.42, P.43, H.44, Y.49, R.57, C.58, C.61, H.62, M.74, C.98, H.102 Ligands: HEC.6 15 PLIP interactions: 15 interactions with chain B, Hydrophobic interactions: B:I.42, B:P.43, B:Y.49, B:R.57 Salt bridges: B:R.30, B:R.30, B:R.33 pi-Stacking: B:H.44, B:H.44, B:H.62, B:H.62, B:H.62, B:H.62 Metal complexes: B:H.44, B:H.62 HEC.6: 23 residues within 4Å: Chain A: L.52, N.53, Y.58 Chain B: R.33, Y.35, P.36, E.37, Q.38, P.39, P.40, L.59, H.62, M.74, I.75, S.76, H.79, R.95, Y.96, F.97, C.98, C.101, H.102 Ligands: HEC.5 21 PLIP interactions: 3 interactions with chain A, 18 interactions with chain B, Hydrophobic interactions: A:L.52, A:Y.58, A:Y.58, B:P.40, B:L.59, B:H.62, B:I.75 Hydrogen bonds: B:E.37, B:Q.38, B:Q.38 Salt bridges: B:R.33, B:R.33 pi-Stacking: B:H.79, B:H.79, B:H.102, B:H.102 pi-Cation interactions: B:H.79, B:R.95, B:H.102 Metal complexes: B:H.79, B:H.102

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Arnoux, P. et al., Structural and Redox Plasticity in the Heterodimeric Periplasmic Nitrate Reductase. Nat.Struct.Biol. (2003)

Release Date

2003-10-09

Peptides

PERIPLASMIC NITRATE REDUCTASE: A
DIHEME CYTOCHROME C NAPB MOLECULE: NITRATE REDUCTASE: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PERIPLASMIC NITRATE REDUCTASE

DIHEME CYTOCHROME C NAPB MOLECULE: NITRATE REDUCTASE

Related Entries With Identical Sequence